Roughness only in some parts
You could do this by creating a black and white mask and using it as the factor of a mix shader to mix the water with the rough water.


First add an image texture node. 
Click new to add a black image. 
Then plug this into the material output. 
Then go to the texture paint workspace. 
Paint the areas you want rough in white.  
Save this black and white image.
Go back to the shading workspace.
Add a mix shader
Plug you black and white image into the fac input
Plug you water material into the top shader input of the mix shader node
Add another Principled BDSF shader and increase its roughness
Plug this into the bottom shader input of the mix shader node


This is the result you'll get:

 

Of course, from here you can make the rough shader more interesting with colour/bump/etc but this is the basic setup!